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In reticular chemistry, molecular building blocks are designed to create crystalline open frameworks. A key principle of reticular chemistry is that the most symmetrical networks are the likely outcomes of reactions, particularly when highly symmetrical building blocks are involved. The strategy of synthesizing low-dimensional networks aims to reduce explicitly the symmetry of the molecular building blocks. Here we report the spontaneous formation of hydrogen-bonded fibrous structures from trigonal prismatic building blocks, which were designed to form three-dimensional crystalline networks on account of their highly symmetrical structures. Utilizing different microscopic and spectroscopic techniques, we identify the structures at the early stages of the assembly process in order to and understand the growth mechanism. The symmetrical molecular building blocks are incorporated preferentially in the longitudinal direction, giving rise to anisotropic hydrogen-bonded porous organic nanotubes. Entropy-driven anisotropic growth provides micrometer-scale unidirectional nanotubes with high porosity. By combining experimental evidence and theoretical modeling, we have obtained a deep understanding of the nucleation and growth processes. Our findings offer fundamental insight into the molecular design of tubular structures. The nanotubes evolve further in the transverse directions to provide extended higher-order fibrous structures [nano- and microfibers], ultimately leading to large-scale interconnected hydrogen-bonded fiber-like structures with twists and turns. Our work provides fundamental understanding and paves the way for innovative molecular designs in low-dimensional networks.

Elicitation of effective antitumor immunity following cancer vaccination requires the selective activation of distinct effector cell populations and pathways. Here we report a therapeutic approach for generating potent T cell responses using a modular vaccination platform technology capable of inducing directed immune activation, termed the Protein-like Polymer (PLP). PLPs demonstrate increased proteolytic resistance, high uptake by antigen-presenting cells (APCs), and enhanced payload-specific T cell responses. Key design parameters, namely payload linkage chemistry, degree of polymerization, and side chain composition, were varied to optimize vaccine formulations. Linking antigens to the polymer backbone using an intracellularly cleaved disulfide bond copolymerized with a diluent amount of oligo(ethylene glycol) (OEG) resulted in the highest payload-specific potentiation of antigen immunogenicity, enhancing dendritic cell (DC) activation and antigen-specific T cell responses. Vaccination with PLPs carrying either gp100, E7, or adpgk peptides significantly increased the survival of mice inoculated with B16F10, TC-1, or MC38 tumors, respectively, without the need for adjuvants. B16F10-bearing mice immunized with gp100-carrying PLPs showed increased antitumor CD8+T cell immunity, suppressed tumor growth, and treatment synergy when paired with two distinct stimulator of interferon gene (STING) agonists. In a human papillomavirus-associated TC-1 model, combination therapy with PLP and 2′3′-cGAMP resulted in 40% of mice completely eliminating implanted tumors while also displaying curative protection from rechallenge, consistent with conferment of lasting immunological memory. Finally, PLPs can be stored long-term in a lyophilized state and are highly tunable, underscoring the unique properties of the platform for use as generalizable cancer vaccines.

An important goal of systems and synthetic biology is to produce high value chemical species in large quantities. Microcompartments, which are protein nanoshells encapsulating catalytic enzyme cargo, could potentially function as tunable nanobioreactors inside and outside cells to generate these high value species. Modifying the morphology of microcompartments through genetic engineering of shell proteins is one viable strategy to tune cofactor and metabolite access to encapsulated enzymes. However, this is a difficult task without understanding how changing interactions between the many different types of shell proteins and enzymes affect microcompartment assembly and shape. Here, we use multiscale molecular dynamics and experimental data to describe assembly pathways available to microcompartments composed of multiple types of shell proteins with varied interactions. As the average interaction between the enzyme cargo and the multiple types of shell proteins is weakened, the shell assembly pathway transitions from (i) nucleating on the enzyme cargo to (ii) nucleating in the bulk and then binding the cargo as it grows to (iii) an empty shell. Atomistic simulations and experiments using the 1,2-propanediol utilization microcompartment system demonstrate that shell protein interactions are highly varied and consistent with our multicomponent, coarse-grained model. Furthermore, our results suggest that intrinsic bending angles control the size of these microcompartments. Overall, our simulations and experiments provide guidance to control microcomparmtent size and assembly by modulating the interactions between shell proteins.

We investigate the usage of polyelectrolyte complex materials for water remediation purposes, specifically their ability to remove nanoplastics from water, on which there is currently little to no prior research. We demonstrate that oppositely charged random copolymers are effective at quantitatively removing nanoplastic contamination from aqueous solution. The mechanisms underlying this remediation ability are explored through computational simulations, with corroborating quartz crystal microbalance adsorption experiments. We find that hydrophobic nanostructures and interactions likely play an important role.

Size-asymmetric binary charged colloidal solutions can assemble into ionic colloidal crystals. These are often stabilized by ionic-type bonding, where the components with smaller size and charge sit at fixed points within the lattice of large particles. Here, we study the transition termed ionic to metallic bonding transition, by which the lattice of the smaller component melts while the crystal of the large particles is preserved, as in metallic bonding. We simulate a charged colloidal crystal in equilibrium with a solution containing small colloidal particles and counterions using the Coulomb interaction between the finite-size components. We find ionic to metallic first-order transitions by increasing either the temperature or the concentration of the small particles in the solution. The transition is accompanied by a lattice expansion and increased absorption of small particles into the crystal. We compute the free energies of the ionic and metallic states using the Madelung constant and Wigner–Seitz cell approaches, respectively, combined with the quasi-harmonic lattice model. The calculation reproduces the simulated transition and reveals that the enthalpic gain is more pronounced than the entropic gain in the transition from ionic to metallic bonding when material is exchanged with the solution.

Effective control over the thermal behavior and mechanical strength of polymeric materials has been highly sought for decades and continues to this day, particularly with the urgent demand for highly durable energy storage devices and soft electronics, to name a few. Here, we report a simple yet versatile approach to fine-tune the glass transition range of a family of ionomers via their side-chain structure and charge fraction. We analyze ionomers of poly(3-sulfopropyl methacrylate-ran-methyl methacrylate) that are synthesized by conventional free-radical polymerization. Using derivative heat flow curves from differential scanning calorimetry, we find that above a critical low charge-carrying side-chain fraction (fq), the glass transition temperature shifts to higher values and the glass transition breadth increases significantly in response to thermal treatment. After several thermal cycles, values of glass transition breadth as high as 90–104 °C were obtained, and the evolution from one glass transition regime to two distinct, contiguous glass transition regimes was evident. Quenched molecular dynamics simulations elucidate the roles of several key design parameters of the ionomers near the glass transition, specifically the importance of the charge-carrying polymer side chains. Analysis of energetics and structural relaxation dynamics reveals the effects of strong ionic correlations in a low dielectric constant medium and the side-chain mobility on the transition from liquid to supercooled liquid. As fqincreases beyond a critical value and is accompanied by thermal treatment, the local ionic concentrations are more heterogeneous, and the distribution of the ionic cluster sizes becomes broader at the transition point. The resulting enhanced degree of compositional and dynamic heterogeneity leads to a shift in the supercooled liquid transition toward higher temperatures.

The use of surfactants to attract dissolved ions to water surfaces and interfaces is an essential step in both solvent-based and solvent-free separation processes. We have studied the interactions of lanthanide ions in the aqueous subphase with monolayers of dihexadecyl phosphate at air–water interfaces. With heavier lanthanides (atomic number Z≥ 65) in the subphase, the floating layer can be compressed to an area/molecule of about half the molecular cross section, indicating bilayer formation. X-ray fluorescence and reflectivity data support this conclusion. In the presence of lighter lanthanides (Z< 65), only monolayers are observed. Subphase-concentration-dependent studies using Er3+(heavier) and Nd3+(lighter) lanthanides show a stepwise progression, with ions attaching to the monolayer only when the solution concentration is >3 × 10–7M. Above ∼10–5M, bilayers form but only in the presence of the heavier lanthanide. Grazing incidence X-ray diffraction shows evidence of lateral ion–ion correlations in the bilayer structure but not in monolayers. Explicit solvent all-atom molecular dynamics simulations confirm the elevated ion–ion correlation in the bilayer system. This bilayer structure isolates heavier lanthanides but not lighter lanthanides from an aqueous solution and is therefore a potential mechanism for the selective separation of heavier lanthanides.

Protein enzymes have shown great potential in numerous technological applications. However, the design of supporting materials is needed to preserve protein functionality outside their native environment. Direct enzyme–polymer self-assembly offers a promising alternative to immobilize proteins in an aqueous solution, achieving higher control of their stability and enzymatic activity in industrial applications. Herein, we propose a modeling-based design to engineering hydrogels of cytochrome P450 and of PETase with styrene/2-vinylpyridine (2VP) random copolymers. By tuning the copolymer fraction of polar groups and of charged groups via quaternization of 2VP for coassembly with cytochrome P450 and via sulfonation of styrene for coassembly with PETase, we provide quantitative guidelines to select either a protein–polymer hydrogel structure or a single-protein encapsulation. The results highlight that, regardless of the protein surface domains, the presence of polar interactions and hydration effects promote the formation of a more elongated enzyme–polymer complex, suggesting a membrane-like coassembly. On the other hand, the effectiveness of a single-protein encapsulation is reached by decreasing the fraction of polar groups and by increasing the charge fraction up to 15%. Our computational analysis demonstrates that the enzyme–polymer assemblies are first promoted by the hydrophobic interactions which lead the protein nonpolar residues to achieve the maximum coverage and to play the role of the most robust contact points. The mechanisms of coassembly are unveiled in the light of both protein and polymer physical-chemistry, providing bioconjugate phase diagrams for the optimal material design.

Self-organized shells are fundamental in biological compartmentalization. They protect genomic material or enclose enzymes to aid the metabolic process. Studies of crystalline shells have shown the importance of the mechanical properties of building units in the shell morphology. However, the mechanism underlying the morphology of multicomponent assemblies is still poorly understood. Here, we analyze multicomponent closed shells that have different mechanical properties. By minimizing elastic energy, we show that heterogeneous bending rigidities regulate the surface pattern into circular, spikes, and ridge shapes. Interestingly, our continuum elasticity model recovers the patterns that have been proposed in bacterial microcompartments (BMCs), which are self-organized protein shells that aid the breakdown of complex molecules and allow bacteria to survive in hostile environments. In addition, our work elucidates the principles of pattern formation that can be used to design and engineer multicomponent microcompartments with a specific surface distribution of the components.

Bacterial microcompartments compartmentalize the enzymes that aid chemical and energy production in many bacterial species. They are postulated to help bacteria survive in hostile environments. Metabolic engineers are interested in repurposing these organelles for non-native functions. Here, we use computational, theoretical, and experimental approaches to determine mechanisms that effectively control microcompartment self-assembly. We find, via multiscale modeling and mutagenesis studies, the interactions responsible for the binding of hexamer-forming proteins in a model system, the propanediol utilization bacterial microcompartments from Salmonella entericaserovar Typhimurium LT2. We determine how the changes in the microcompartment hexamer protein preferred angles and interaction strengths can modify the assembled morphologies. We demonstrate that such altered strengths and angles are achieved via amino acid mutations. A thermodynamic model provides guidelines to design microcompartments of various morphologies. These findings yield insight in controlled protein assembly and provide principles for assembling microcompartments for biochemical or energy applications as nanoreactors.

Colloidal particles are ubiquitous in biology and in everyday products such as milk, cosmetics, lubricants, paints, or drugs. The stability and aggregation of colloidal suspensions are of paramount importance in nature and in diverse nanotechnological applications, including the fabrication of photonic materials and scaffolds for biological assemblies, gene therapy, diagnostics, targeted drug delivery, and molecular labeling. Electrolyte solutions have been extensively used to stabilize and direct the assembly of colloidal particles. In electrolytes, the effective electrostatic interactions among the suspended colloids can be changed over various length scales by tuning the ionic concentration. However, a major limitation is gelation or flocculation at high salt concentrations. This is explained by classical theories, which show that the electrostatic repulsion among charged colloids is significantly reduced at high electrolyte concentrations. As a result, these screened colloidal particles are expected to aggregate due to short-range attractive interactions or dispersion forces as the salt concentration increases. We discuss here a robust, tunable mechanism for colloidal stability by which large counterions prevent highly charged nanoparticles from aggregating in salt solutions with concentrations up to 1 M. Large counterions are shown to generate a thicker ionic cloud in the proximity of each charged colloid, which strengthens short-range repulsions among colloidal particles and also increases the corresponding renormalized colloidal charge perceived at larger separation distances. These effects thus provide a reliable stabilization mechanism in a broad range of biological and synthetic colloidal suspensions.

Crystalline vesicles are promising nanomaterials due to their mechanical stability in various environments. To control their fabrication, it is essential to understand the effects of different experimental conditions on crystallization. Here we perform atomistic molecular dynamics simulations of anionic lipid membranes of 1,2-dilauroyl-sn-glycero-3-phosphol-l-serine. In the presence of Na+monovalent counterions, we access the phase transition from the liquid-like disordered liquid-crystalline phase to the ordered gel phase by lowering the temperature of the system. The phase transition is conclusivelyevidenced by the scattering structure factor. Quantitativecalculations show that the enhancement of the intertail van der Waals interaction (about −6 kBT) plays a dominant role in driving the phase transition rather than the increase in the cohesive interaction (−0.5 kBT) between lipids and counterions. Meanwhile, in the presence of multivalent counterions of Zn2+or La3+the gel phase is found throughout the temperature range investigated. Moreover, the van der Waals interaction per hydrocarbon group is ∼20% stronger in the gel phase (∼ −1.8 kBTregardless of the counterions) than in the liquid-crystalline phase (−1.5 kBT).

Epitaxial growth of DNA-functionalized nanoparticles is used to grow extended superlattices with a preferred orientation for optimizing the physical properties of metamaterials for real applications. Like any solid in nature, superlattices can contain different kinds of structural defects, which significantly alter their physical properties. Further development of these materials requires a deeper understanding of, as well as precise control over, structural defect formation. Here we use Monte Carlo simulations to conduct a systematic study of the equilibrium structures of the adsorbed nanoparticle monolayers by changing the binding energies of different attachment sites. The simulations show two main results. First, the structural defects form one-dimensional clusters with an exponential length distribution. Second, these linear defects exhibit spontaneous symmetry breaking and undergo a liquid crystal phase transition. Subsequently, a mean-field approach is introduced to provide theoretical descriptions for the system. Our theory matches with the simulation results. We anticipate that this theoretical framework will be highly applicable to other two-dimensional assemblies. Our work demonstrates that defects can be engineered to design two-dimensional superlattices with interesting physical properties.

The encapsulation of enzymes within porous materials has shown great promise, not only in protecting the enzymes from denaturation under nonbiological environments, but also, in some cases, in facilitating their enzymatic reaction rates at favorable reaction conditions. While a number of hypotheses have been developed to explain this phenomenon, the detailed structural changes of the enzymes upon encapsulation within the porous material, which are closely related to their activity, remain largely elusive. Herein, the structural change of cytochrome c (Cyt c) upon encapsulation within a hierarchical metal–organic framework, NU-1000, is investigated through a combination of experimental and computational methods, such as electron paramagnetic resonance, solid-state ultraviolet–visible spectroscopy, and all-atom explicit solvent molecular dynamics simulations. The enhanced catalytic performance of Cyt c after being encapsulated within NU-1000 is supported by the physical and in silico observations of a change around the heme ferric active center.

The surface of proteins is vital in determining protein functions. Herein, a program, Protein Surface Printer (PSP), is built that performs multiple functions in quantifying protein surface domains. Two proteins, PETase and cytochrome P450, are used to validate that the program supports atomistic simulations with different combinations of programs and force fields. A case study is conducted on the structural analysis of the spike proteins of SARS-CoV-2 and SARS-CoV and the human cell receptor ACE2. Although the surface domains of both spike proteins are highly similar, their receptor-binding domains (RBDs) and the O-linked glycan domains are structurally different. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells.

The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein plays a crucial role in binding the human cell receptor ACE2 that is required for viral entry. Many studies have been conducted to target the structures of RBD–ACE2 binding and to design RBD-targeting vaccines and drugs. Nevertheless, mutations distal from the SARS-CoV-2 RBD also impact its transmissibility and antibody can target non-RBD regions, suggesting the incomplete role of the RBD region in the spike protein–ACE2 binding. Here, in order to elucidate distant binding mechanisms, we analyze complexes of ACE2 with the wild-type spike protein and with key mutants vialarge-scale all-atom explicit solvent molecular dynamics simulations. We find that though distributed approximately 10 nm away from the RBD, the SARS-CoV-2 polybasic cleavage sites enhance, viaelectrostatic interactions and hydration, the RBD–ACE2 binding affinity. A negatively charged tetrapeptide (GluGluLeuGlu) is then designed to neutralize the positively charged arginine on the polybasic cleavage sites. We find that the tetrapeptide GluGluLeuGlu binds to one of the three polybasic cleavage sites of the SARS-CoV-2 spike protein lessening by 34% the RBD–ACE2 binding strength. This significant binding energy reduction demonstrates the feasibility to neutralize RBD–ACE2 binding by targeting this specific polybasic cleavage site. Our work enhances understanding of the binding mechanism of SARS-CoV-2 to ACE2, which may aid the design of therapeutics for COVID-19 infection.

Understanding viral assembly pathways is of critical importance to biology, medicine, and nanotechology. Here, we study the assembly path of a system with various structures, the simian vacuolating virus 40 (SV40) polymorphs. We simulate the templated assembly process of VP1 pentamers, which are the constituents of SV40, into icosahedal shells made of N= 12 pentamers (T= 1). The simulations include connections formed between pentamers by C-terminal flexible lateral units, termed here “C-terminal ligands”, which are shown to control assembly behavior and shell dynamics. The model also incorporates electrostatic attractions between the N-terminal peptide strands (ligands) and the negatively charged cargo, allowing for agreement with experiments of RNA templated assembly at various pH and ionic conditions. During viral assembly, pentamers bound to any template increase its effective size due to the length and flexibility of the C-terminal ligands, which can connect to other VP1 pentamers and recruit them to a partially completed capsid. All closed shells formed other than the T= 1 feature the ability to dynamically rearrange and are thus termed “pseudo-closed”. The N= 13 shell can even spontaneously “self-correct” by losing a pentamer and become a T= 1 capsid when the template size fluctuates. Bound pentamers recruiting additional pentamers to dynamically rearranging capsids allow closed shells to continue growing viathe pseudo-closed growth mechanism, for which experimental evidence already exists. Overall, we show that the C-terminal ligands control the dynamic assembly paths of SV40 polymorphs.

Complexation of oppositely charged macromolecules is essential in several biological phenomena. Recent reports have demonstrated the importance of DNA local flexibility in governing liquid–liquid phase separation (LLPS), a ubiquitous phenomenon thought to drive membraneless cellular organization. Inspired by this, we perform coarse-grained molecular dynamics simulations to study the role of chain flexibility in the complexation of short negatively charged polyelectrolytes with long positively charged polyelectrolytes. At low ionic strengths, spontaneous segregation of chains into a condensed (polymer-rich) phase and a supernatant (polymer-depleted) phase is observed. When both the polyanion and polycation are flexible (flexible–flexible complex), denser complexes with a higher degree of structural correlation form, with fewer free chains released into the supernatant, compared to the case when the polyanion is rigid (rigid–flexible complex), in agreement with the LLPS experiments. Free chains are in rapid exchange between the supernatant and the condensed phase. The partitioning of salt ions in the two phases depends on chain flexibility, with salt ions partitioned more into the condensed phase for flexible–flexible complexes. Interestingly, at intermediate to high salt concentrations, flexible–flexible complexes form multiple equilibrium finite-size clusters, suggesting nanophase to microphase segregated structures, while rigid–flexible complexes tend to condense into a single complex. The results provide molecular-level insights into LLPS of asymmetric polyelectrolyte complexation and give guidelines for assembling oppositely charged macromolecules with different degrees of molecular flexibility.

Solid polymer electrolytes are considered a promising alternative to traditional liquid electrolytes in energy storage applications because of their good mechanical properties, and excellent thermal and chemical stability. A gap, however, still exists in understanding ion transport mechanisms and improving ion transport in solid polymer electrolytes. Therefore, it is crucial to bridge composition–structure and structure–property relationships. Here, we demonstrate that size asymmetry, λ, represented by the ratio of counterion to charged monomer size, plays a key role both in the nanostructure and in the ionic dynamics. More specifically, when the nanostructure is modified by an external electric field such that the mobility cannot be described by linear response theory, two situations arise. The ionic mobility increases as λ decreases (small counterions) in the weak electrostatics (high dielectric constant) regime, whereas in systems with strong electrostatic interactions, ionomers with higher size symmetry (λ ≈ 1) display higher ionic mobility. Moreover, ion transport is found to be dominated by the hopping of the ions and not by moving ionic clusters (also known as “vehicular” charge transport). These results serve as a guide for designing ion-containing polymers for ion transport related applications.

Label-free in situX-ray scattering from protein spherical nucleic acids (Pro-SNAs, consisting of protein cores densely functionalized with covalently bound DNA) was used to elucidate the enzymatic reaction pathway for the DNase I-induced degradation of DNA. Time-course small-angle X-ray scattering (SAXS) and gel electrophoresis reveal a two-state system with time-dependent populations of intact and fully degraded DNA in the Pro-SNAs. SAXS shows that in the fully degraded state, the DNA strands forming the outer shell of the Pro-SNA were completely digested. SAXS analysis of reactions with different Pro-SNA concentrations reveals a reaction pathway characterized by a slow, rate determining DNase I-Pro-SNA association, followed by rapid DNA hydrolysis. Molecular dynamics (MD) simulations provide the distributions of monovalent and divalent ions around the Pro-SNA, relevant to the activity of DNase I. Taken together, in situSAXS in conjunction with MD simulations yield key mechanistic and structural insights into the interaction of DNA with DNase I. The approach presented here should prove invaluable in probing other enzyme-catalyzed reactions on the nanoscale.

Light-sensitive particles have been shown to stratify in solution in a way that changes the colour of the whole suspension. The system forms a colour-changing ink that could make electronic paper a viable technology.

We demonstrate that a highly charged polyelectrolyte confined in a spherical cavity undergoes reversible transformations between amorphous conformations and a four-fold symmetry morphology as a function of dielectric mismatch between the media inside and outside the cavity. Surface polarization due to dielectric mismatch exhibits an extra “confinement” effect, which is most pronounced within a certain range of the cavity radius and the electrostatic strength between the monomers and counterions and multivalent counterions. For cavities with a charged surface, surface polarization leads to an increased amount of counterions adsorbed in the outer side, further compressing the confined polyelectrolyte into a four-fold symmetry morphology. The equilibrium conformation of the chain is dependent upon several key factors including the relative permittivities of the media inside and outside the cavity, multivalent counterion concentration, cavity radius relative to the chain length, and interface charge density. Our findings offer insights into the effects of dielectric mismatch in packaging and delivery of polyelectrolytes across media with different relative permittivities. Moreover, the reversible transformation of the polyelectrolyte conformations in response to environmental permittivity allows for potential applications in biosensing and medical monitoring.

Rebinding kinetics of molecular ligands plays a key role in the operation of biomachinery, from regulatory networks to protein transcription, and is also a key factor in design of drugs and high-precision biosensors. In this study, we investigate initial release and rebinding of ligands to their binding sites grafted on a planar surface, a situation commonly observed in single-molecule experiments and that occurs in vivo, e.g., during exocytosis. Via scaling arguments and molecular dynamic simulations, we analyze the dependence of nonequilibrium rebinding kinetics on two intrinsic length scales: the average separation distance between the binding sites and the total diffusible volume (i.e., height of the experimental reservoir in which diffusion takes place or average distance between receptor-bearing surfaces). We obtain time-dependent scaling laws for on rates and for the cumulative number of rebinding events. For diffusion-limited binding, the (rebinding) on rate decreases with time via multiple power-law regimes before the terminal steady-state (constant on-rate) regime. At intermediate times, when particle density has not yet become uniform throughout the diffusible volume, the cumulative number of rebindings exhibits a novel, to our knowledge, plateau behavior because of the three-dimensional escape process of ligands from binding sites. The duration of the plateau regime depends on the average separation distance between binding sites. After the three-dimensional diffusive escape process, a one-dimensional diffusive regime describes on rates. In the reaction-limited scenario, ligands with higher affinity to their binding sites (e.g., longer residence times) delay entry to the power-law regimes. Our results will be useful for extracting hidden timescales in experiments such as kinetic rate measurements for ligand-receptor interactions in microchannels, as well as for cell signaling via diffusing molecules.

Protein aggregation has been observed inside cells and holds true for membraneless organelles. The precise understanding of protein dimerization is a prerequisite for manipulating protein aggregation, which is promising for elevating enzyme concentration to enhance their catalytic performance. Here, the dimerization of two industrially important enzymes of cytochrome P450 (P450) and organophosphorus hydrolase (OPH) is investigated using all-atom explicit solvent molecular dynamics simulations, umbrella sampling, and protein–protein docking calculations. The calculated potentials of mean force of dimer–monomer dissociation demonstrate that the dimeric forms are more stable with the free energy barrier of around 60 kJ/mol for P450 and 101 kJ/mol for OPH. The docking calculations on the OPH dimer evidence the uniqueness of the native orientation. The protein dimers form “mirror”-like orientations with some degree of rotation. Such signature orientations are interpreted based on the predominant polar amino acids in the contact regime. In the dimer conformations, the active sites are exposed. This work highlights the crucial roles of the polar and nonpolar protein surface domains to form enzymatically active protein dimer aggregates. Our work will potentially aid the design of molecules that can deliver and protect native protein function in various environments.

Quantitatively understanding the self-assembly of amphiphilic macromolecules at liquid–liquid interfaces is a fundamental scientific concern due to its relevance to a broad range of applications including bottom-up nanopatterning, protein encapsulation, oil recovery, drug delivery, and other technologies. Elucidating the mechanisms that drive assembly of amphiphilic macromolecules at liquid–liquid interfaces is challenging due to the combination of hydrophobic, hydrophilic, and Coulomb interactions, which require consideration of the dielectric mismatch, solvation effects, ionic correlations, and entropic factors. Here we investigate the self-assembly of a model block copolymer with various charge fractions at the chloroform–water interface. We analyze the adsorption and conformation of poly(styrene)-block-poly(2-vinylpyridine) (PS-b-P2VP) and of the homopolymer poly(2-vinylpyridine) (P2VP) with varying charge fraction, which is controlled via a quaternization reaction and distributed randomly along the backbone. Interfacial tension measurements show that the polymer adsorption increases only marginally at low charge fractions (<5%) but increases more significantly at higher charge fractions for the copolymer, while the corresponding randomly charged P2VP homopolymer analogues display much more sensitivity to the presence of charged groups. Molecular dynamics (MD) simulations of the experimental systems reveal that the diblock copolymer (PS-b-P2VP) interfacial activity could be mediated by the formation of a rich set of complex interfacial copolymer aggregates. Circular domains to elongated stripes are observed in the simulations at the water–chloroform interface as the charge fraction increases. These structures are shown to resemble the spherical and cylindrical helicoid structures observed in bulk chloroform as the charge fraction increases. The self-assembly of charge-containing copolymers is found to be driven by the association of the charged component in the hydrophilic block, with the hydrophobic segments extending away from the hydrophilic cores into the chloroform phase.

We examine the effects of ionic correlations and dielectric mismatch on the miscibility of ionomer blends with a hybrid ionomer blend thermodynamic liquid state theory approach. The ionomer (A) has a dielectric constant ϵAand low charge fraction (<10%). First, explicit ions coarse-grained molecular dynamics simulations with no dielectric mismatch verify that ionic correlations lead to segregation, in agreement with the theory, which includes nonlinear and many-body effects. Then, the extended theory that incorporates dielectric mismatch shows that strong ionic correlations dominate the phase behavior when the dielectric mismatch is low. However, solvation effects dominate when the mismatch is high (ϵA≫ ϵB), where the preference of the ions to be solvated in a higher dielectric medium is balanced by the entropic driving force for a uniform dielectric constant throughout the system. When salt is added as a third component, dielectric mismatch is significant only at low salt concentrations.